Couldn’t the retailer just look up when the cookie was set? If it was set during some window before the user had items in their cart, pay the affiliate. If it was set after, or long in the past, don’t pay.
Then it's a game of trying to find ways to not pay your affiliates. Do you want to be the retailer than gets known in the affiliate space for trying to find loopholes not to pay what they said they would? People would stop promoting your site. You might as well shut down your affiliate program if you're going to not pay your affiliates sometimes.
It doesn’t look like these guys (or most “affiliates”) are actually promoting the site or driving traffic. They’re just dipping their spoons in the existing money river.
I have considered this as a possibility when it comes to shopping through affiliate portals (such as a credit card) in order to get bonus points.
I usually open a private window to mitigate them doing something less the super sophisticated.
In my case, I can often get the same item (or similar quality item) for same or near price, I value the extra points a retailer that participates through the affiliate program provides, and I choose that retailer.
It's fairly common for people to abandon the cart and come back later to complete the purchase, not always coupon related. Especially true with non-impulse purchases costing 3 figures or more.